Hi, Indeed, although having the craype-ivybridge module loaded (when perhaps it was not loaded at CMake time) does not look like it would help.
Mark On Mon, Oct 5, 2015 at 5:47 PM Szilárd Páll <pall.szil...@gmail.com> wrote: > On Mon, Oct 5, 2015 at 6:15 AM, kevin chen <fch6...@gmail.com> wrote: > > > Dear Gromacs users, > > > > I am trying to build gromacs on our latest supercomputer CRAY XC40, but > the > > following errors using gcc and fftw. Here's my list of module loaded and > > install script, can anyone give any instructions? > > > > ========================================================================= > > Currently Loaded Modulefiles: > > 1) modules/3.2.6.7 8) gcc/4.9.3 > > 15) xpmem/0.1-2.0502.55507.3.2.ari > > 2) eswrap/1.1.0-1.020200.1231.0 9) cray-libsci/13.1.0 > > 16) dvs/2.5_0.9.0-1.0502.1873.1.145.ari > > 3) switch/1.0-1.0502.54233.2.96.ari 10) > > udreg/2.3.2-1.0502.9275.1.12.ari 17) alps/5.2.1-2.0502.9041.11.6.ari > > 4) craype-network-aries 11) > ugni/5.0-1.0502.9685.4.24.ari > > 18) rca/1.0.0-2.0502.53711.3.127.ari > > 5) craype/2.4.1 12) > > pmi/5.0.8-1.0000.10843.170.1.ari 19) atp/1.8.3 > > 6) cray-mpich/7.2.4 13) > > dmapp/7.0.1-1.0502.9501.5.219.ari 20) PrgEnv-gnu/5.2.40 > > 7) craype-ivybridge 14) > > gni-headers/3.0-1.0502.9684.5.2.ari 21) fftw/3.3.4.4 > > > =========================================================================== > > export CXX=`which cc` > > export CC=`which cc` > > export MPICC=`which cc` > > export F77=`which ftn` > > export INSTALL_PATH=/home1/03024/chenk/Software/Gromacs/install > > > > mkdir g_single_parallel > > cd g_single_parallel > > > > > > /home1/03024/chenk/Software/cmake/install/bin/cmake .. \ > > -DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \ > > -DGMX_FFT_LIBRARY=fftw3 \ > > -DGMX_X11=OFF \ > > -DBUILD_SHARED_LIBS=OFF \ > > -DGMX_PREFER_STATIC_LIBS=ON \ > > -DGMX_BUILD_MDRUN_ONLY=OFF \ > > -DGMX_MPI=ON -DGMX_OPENMP=ON \ > > -DGMX_XML=OFF \ > > -DGMX_SOFTWARE_INVSQRT=OFF \ > > -DGMX_SKIP_DEFAULT_CFLAGS=ON \ > > -DCMAKE_C_COMPILER=cc \ > > -DCMAKE_C_FLAGS="-fomit-frame-pointer -finline-functions > -funroll-all-loops > > -O3 " \ > > -DCMAKE_CXX_COMPILER=cc \ > > -DCMAKE_CXX_FLAGS="-O3" \ > > > > "cc" should typically be a Cray compiler wrapper, so Mark's guess about the > compiler rather than the wrapper being using is likely not the reason for > the errors. > > I think the issue is that you seem to want to override _all_ GROMACS > default compiler flags (BTW, amy I ask why do you want to do that?). In any > case, if you believe you have something that works better for you or you > want to test flags, you're free to do that, but you can't omit essential > flags. In this case you seem to be missing those that enable SIMD > intrinsics, that is -mavx2 (or in some gcc versions that's not supported, > so you need to use -march=core-avx2). > > AFAICT you're not adding any of those flags and that would explain why does > your build fail to recognize SIMD instrinsics. > > Let me know if your issue is solved and it would be interesting to hear if > found a combination of flags that gives better performance than our default > ones! > > Cheers, > -- > Szilárd > > > > > -DGMX_DEFAULT_SUFFIX=ON \ > > -DGMX_EXTERNAL_BOOST=OFF \ > > -DGMX_BUILD_SHARED_EXE=off > > > > make -j 12 > > make install > > ========================================================================= > > Error messages: > > > > In file included from > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h: > > In function 'gmx_simd_rsqrt_iter_f': > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:159:1: > > error: inlining failed in call to always_inline '_mm256_fnmadd_ps': > target > > specific option mismatch > > _mm256_fnmadd_ps (__m256 __A, __m256 __B, __m256 __C) > > ^ > > In file included from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118:0, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:61:36: > > error: called from here > > #define gmx_simd_fmadd_f _mm256_fmadd_ps > > ^ > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h:146:12: > > note: in expansion of macro 'gmx_simd_fmadd_f' > > return gmx_simd_fmadd_f(gmx_simd_fnmadd_f(x, gmx_simd_mul_f(lu, lu), > > gmx_simd_set1_f(1.0f)), gmx_simd_mul_f(lu, gmx_simd_set1_f(0.5f)), lu); > > ^ > > In file included from > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118, > > from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62: > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:63:1: > > error: inlining failed in call to always_inline '_mm256_fmadd_ps': target > > specific option mismatch > > _mm256_fmadd_ps (__m256 __A, __m256 __B, __m256 __C) > > ^ > > In file included from > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:63:0: > > > > > /home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h:146:5: > > error: called from here > > return gmx_simd_fmadd_f(gmx_simd_fnmadd_f(x, gmx_simd_mul_f(lu, lu), > > gmx_simd_set1_f(1.0f)), gmx_simd_mul_f(lu, gmx_simd_set1_f(0.5f)), lu); > > ^ > > [ 51%] Building C object > > src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.c.o > > make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/bondfree.c.o] > > Error 1 > > make[2]: *** Waiting for unfinished jobs.... > > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > > make: *** [all] Error 2 > > [ 0%] Building C object > > src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/bondfree.c.o > > In file included from > > > > > /opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0, > > > > ========================================================================= > > > > Thanks in advance! > > > > Kevin > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? 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